Through the Eyes of Unit 01
by drew6406
Summary: AU. A transfer student named Arika comes into Shinji's life and saves him from committing suicide two years before the angel war. As quickly as she came she is kidnapped and wakes up in Nerv's lab. Little did she know she would become the berserker he would ride into battle. And then become the enemy humanity swore to fight along with him. This is their story of becoming a legend.
1. Prologue: The Sinister Plot

**Evangelion belongs to Ginimax. I own nothing but the story and my own characters.**

 **All right here's the first chapter to my third story. Now I know I haven't updated the other two, but right now thoes stories I have writers block. Until then this will be the active story. Anyway, let the story begin.**

It's been many years now since the day my lover's life could've ended. Many of my friends, and those I considered family, are now all but gone. Old enemies of the past are dead, but not forgotten. Speaking of which, I should tell the story of how we became 'them.' We didn't ask to be immortal… to a certain point, but that's how it is. Every so many thousands of years finding a planet to spread new life. Then moving on to the next. Anyway I'm getting ahead of myself here.

It all started with a group called Selee, a group of arrogant bastards who wanted to be gods among men. Force instrumentality on humanity to reach a divine status. With what they called The Dead Sea Scrolls, the instructions to Second and Third Impact, they would carry out their scenario. The awakening and disintegration of Adam, the first angel of the seventeen supposed messengers of god, went according to plan. Second Impact, September 13, 2000: half of the human population of the world was laid to waste. Cities were submerged, and coastlines changed by the rising sea levels of Antarctica's vaporization. A true dead sea formed at the bottom of the Southern Hemisphere. Perpetual summer covered the rest of the world due to the earth's axis shifting. The rest of Selee's plan was to control Third Impact, by eliminating the rest of the angels, except for Lilith, the second angel. The scrolls predicted that the fifteen other messengers would come to Japan in the year 2015. There was a problem. Selee needed to destroy the angels when the time came, but how? They needed to form a scientific military organization (Gerin at the time, later NERV) tasked with building constructs for war using cloned DNA from the first two angels. These biological weapons would come to be known as Evangelion. Towering, armored, humanoid giants, piloted by tiny human beings.

Creating them however was a whole other challenge. NERV performed thousands upon thousands of tests, many of them seen as 'breakthroughs.' But the final product always ended in failure. Each failed Eva was brought to Terminal Dogma and stripped of its flesh, leaving nothing but its bones, cybernetics, and armor. With so many robotic skeletons reminding NERV of their failures, it was no wonder they called it the Eva graveyard. The scientists would come so close to perfection, but get the same problem. They couldn't control their creations. They would have to shut it down, or it would damage the test chamber and fall apart from going berserk.

More months went by without any positive results, until one day, one of the scientists got an idea. Why not base a control system on having a human soul absorbed into the core. And so the contact experiment was born. No one knows who the candidate was, because the commander picked the subject and loaded them into the entry plug before the test was ready. NERV went through with it anyway, and got mixed results. Upon completion of the test, the unit preceded to go on a rampage. It broke free of its restraints and bashed the viewing window, destroying the glass. It then shut down and began to deteriorate, but more slowly than the previous attempts. The brighter side was that pilots could be identified by how much they synchronized with the core soul and how similar their DNA was. The Eva would mark the place as the first true prototype to the future units. Thus the Eva got its name: Unit 00.

Unit 00 still had the drawbacks the others had. If not treated properly, the Eva would fall apart, like the other failed Evas, in a year's time. The new commander, Gendo Ikari, would not have this. So he ordered project E to come up with a plan B for constructing the Evas, a method for making them last longer and cost less to build. It was not until May 16th, 2003 that they found a solution, one even more sinister than forcing a soul to be absorbed into the core. Scientists figured if they could upscale an already stable humanoid being then it would be able to fit the role of an Eva. The scientists wanted beings who were still growing physically and mentally, so they chose adolescent humans. That's right! Teenagers! They would conduct a test to see if they're fit on all levels. Then inject them with angel DNA to bring about the physical change to Eva status. Lock them in armor and restraints, add cybernetics and the entry plug, and do the contact experiment. Voila! An Evangelion.

The first test of the ECP, Evangelion Conversion Project, didn't start until late October in NERV Berlin. The test went on for 96 hours without a hitch. The end result was a new red and orange eva (later known as Unit 02), an out of their mind scientist, and one psychologically scarred redhead girl. The final result may have been a success, but NERV paid a heavy price for the accomplishment. Most of the staff from every NERV branch resigned after hearing that a child had been turned into a biological weapon. Because of this, the true plan of the program became top secret and the ex-staff members 'disappeared' and were replaced. The commander then launched a examination program to all high schools within proximity of Nerv facilities. If a student passed the test with more than 90%, they would be slated for the ECP.

One evening in 2004, Yui Ikari, the commander's wife, was driving home from Nerv. In the backseat young Shinji, age 4, slept peacefully. The drive was going smoothly until a drunk driver swerved and collided with the driver's side of the car. Shinji was nearly unscathed, but his mother was rushed to Nerv's hospital. Gendo heard the news and rushed there immediately. As soon as he arrived, a doctor informed him that Yui was dying from severe blood loss. As a final attempt to save her, he had her taken to the lab, and forcefully absorbed into a waiting core made from Lilith's DNA. Shinji watched in terror as alarms went off and they failed to retrieve her. If things weren't bad enough, the next day he was abandoned at a train station to wait for his teacher. Gendo may have left his son, but he spent the next 11 years devising a plan to use Third Impact to get Yui back. All he needed to do was get ahold of both angels, defeat the rest, make ayanami clones, make his son the third child, and create a Lilith DNA Evangelion for him to pilot. As the years passed, he was able to check off the steps of his scenario. By 2013, the only thing left was the candidate for Unit 01. But he would find his chosen subject once the year's examination test finished in Tokyo 3 high school.

 **I'm sorry not having any real dialogue in this chapter, but the next will have some.**

 **P.O.V. Will also switch in places. Next chapter: The only True Friend**


	2. Chapter 1: The Only True Friend

**Sorry for the long wait. I had a lot of things going on in my life at the time. But to make up for the long gap, here's a long chapter. :D**

* * *

 **Chapter 1 The only true friend**

* * *

It was a Tuesday in May, 2013, and there wasn't a single cloud in sight. Cicadas buzzed here and there, down the street. A light breeze rustled the leaves of nearby trees. The air was rich with the smell of spring. All was calm until an alarm clock from one of the houses blared. The occupant, a teenage girl, jerked awake and scrambled out of bed. Today was her first day of school after moving from Tokyo 2, and she was not going to be late. The young Arika Shimizu was a whirlwind of movement as she raced around the house to get her things together for the day. Luckily for her, her grandmother was a heavy sleeper; otherwise, Arika would have been in for a scolding for making so much noise. With everything gathered, she quickly made breakfast, then sped out the door. "I can't be late or else I won't make a good first impression to the teacher."

As she ran down the street, her light green hair, the product of an unexpected genetic mutation, blew back in the wind. Every now and then, people would laugh, gawk, or just stare at her hair, but this didn't bother her. After living with it for years, she no longer cared what people said, Beside that unimportant issue, nothing was really wrong in her life, except that she didn't have any friends. This she hoped to fix once the school year kicked off.

"Only a block away now. I can even see the front gate." And so Arika continued to race down the road.

* * *

Meanwhile at Nerv, in a big room with dim lighting that gives a foreboding air, sits alone desk. A man with a beard and orange tinted glasses sat there. This man was none other than the supreme commander of Nerv. Gendo Ikari. He was looking at the latest version of the P.E.C.T., Project: Evangelion Conversion Test, code named: Physical Evaluation Capability Test. Although his face didn't show it, he was concerned that he didn't have a candidate to make Unit 01. He already had his son signed off as the pilot, and a core ready, but he still needed the actual evangelion. Unit 01 was to be a big piece of his scenario to get Yui back. To make things even worse, the third angel was going to appear in two years' time. He needed the perfect candidate, one that would score 99 or 100 on the test. Only one compatible with the Lilith DNA could hope to score so well.

He looked up from his desk to see his second-in command, Fuyutsuki, enter the office.

"Have the arrangements been made for Shinji to enroll in Tokyo 3 High School?"

"Yes. They were sent out last month with all of the other information on enrolling students. He started two weeks ago."

"Good. Now onto other things."

"Speaking of which. I hear a new student has enrolled and is starting today."

"Irrelevant"

"Ikari. I wouldn't say so because they are starting today, the day the of P.E.C.T. Perhaps they are your 'perfect' candidate."

"We will see if this comes to fruition or not. I'm certain a candidate will show."

* * *

At school, Arika was discussing her schedule and the day's events with the principal.

"I welcome you, Arika Shimizu, to our high school." he said "Here are a few papers for you. The first has all of the school's policies, the second is schedule of all your classes, and the third has details to your home room, locker number, and ID."

"Thank you sir." Arika said. "Is there anything else I need to know about?"

"Oh that's right there is also a test you will be taking last period along with the rest of the students. This test is called the P.E.C.T. The Physical Evaluation Capability Test."

"What's the purpose of this test?"

"It's to test your physical and mental strengths."

"Ok. If I have any problems, I'll come and see you for changes?"

"Of course. See you later. Please do well."

* * *

After having to introduce herself to her morning classes, lunch was a welcome break. Most of the students ate outside, while some ate in the classroom. As she looked around, she saw that no one decided to head for the roof to eat. Craving solitude, she started her way up the stairs. When she reached the top, she noticed that the door was ajar. As she pushed it further open, she saw a boy at the edge of the roof. He was wearing a white dress shirt, black pants, and had short brown hair. Something in his posture told her that he wasn't just enjoying the view. He was going to jump. She ran forward and cried out, "STOP! DON'T DO IT! It's Not Worth it!"

* * *

This was it. Nothing stood in Shinji's way of taking his life. "From mother being killed by that drunk driver, to father abandoning me at that train station to wait for my teacher," Shinji thought. "No one talked to me. No one even cared. I guess no one will care if I'm gone either. I'm going to jump. One… Two… Thr…"

"STOP! DON'T DO IT! It's Not Worth it!"

As soon as he heard that shout, Shinji turned around to face the voice. On the other side of the fence, he saw a girl he did not recognize standing there crying. She wore the standard girls' uniform for the school, but her deep blue eyes and shoulder-length light green hair caught his eye immediately.

'Since when has there been a girl in this school with green hair?' Shinji thought, as she stared at him, her face full of horror.

"Why?! … Why must you throw your life away on a beautiful day like this?!" Arika sobbed.

This caught Shinji off guard. " … uh …"

"You have so much to live for, endless possibilities, a future not set in stone. You sho…"

"Why should I listen to you! No one ever listens to me! They never understand how much pain I'm in!" Shinji interrupted."All they ever do is cause more pain, so why can't they leave me alone! Why! WHY!..."

"Because they know there's something other than pain. There's the joy, happiness and love friends bring when people commune with each other! If it bothers you so much, then I'll listen. I give you my ears and undivided attention. I won't judge you for what you say, so let it all out. Come back to the light side of the fence. Come to me and I'll listen to the story of your life."

'What's with this girl? She's not like anyone else.' Shinji pondered. "Okay," he answered reluctantly.

And so Shinji told Arika about his past up to the point where he made his decision to jump to his death.

"Your parents remind me so much of mine. But unlike you, my father is dead too They were both very kind people I can assure you. Both of them died when I was five… They committed suicide right in front of me… I still don't know why. but that's why I take any chance I get to stop it from happening in front of me again." She looked away for a moment, as if overwhelmed by her own intensity. "Anyway, my grandma took me in, but she was a mean old witch. So I try to live my life to the fullest and not let anything get in my way, despite everything." explained Arika. Shinji was surprised. He was amazed that this girl had dealt with more shit than he had gone through.

"Wow. And I thought I had it worse… Oh. I never really got your name by chance."

"How rude of me. My name is Arika Shimizu. And yours?"

My name is Shinji Ikari… Wait a minute. Aren't you the new student that transferred here from Tokyo 2?"

"Indeed I am. My grandma and I moved here two weeks ago, and I don't think we're leaving anytime soon." Arika answered."Hay. You know what Shinji?"

"What?"

"You and I are going to be great friends. My first best friend."

"I haven't really had any friends before." said Shinji nervously.

"Well today's a first. Today's a first for a lot of things."

Just then the school bell rang.

"Oh well look at the time. We need to return to class. Here I'll walk with you part of the way."

"Th… Thank you Shimizu."

"Arika, Shinji. Remember we're friends now."

"Right. Arika."

The two continued to walk

"By the way, Arika, why is your hair light green?"

She gave him a quizzical look, as if she didn't get the question all that often. "Why is it light green? Well it's light green because of an unexpected gene mutation. The genes for hair color mutated, and my hair turned light green."

"Hmmm," he said, with a half-smile. "I guess that doesn't happen every day now does it."

A few minutes of silence passed before Shinji spoke again.. "I heard there's a test last last period."

"Yes I was informed."

"I'm not too sure I'm going to pass."

"Of course you're going to pass because I'm going to pass." She gave him a stern look. "Cheer up. Being pessimistic about it isn't going to get you anywhere. As the song goes: Always look on the bright side of life."

He just nodded.

"Listen. I know things can be hard at times, but promise me this. Promise me that you won't try to kill yourself just because you think the pain in the world is unbearable. Ok?"

"Ok, Arika."

"Look, Shinji. I'll always be there for you. Even when I'm not around I'll be there in spirit, because that's what friends are for. Ok.?"

"Alright."

"Good. Now let's go pass that test! See you tomorrow, Shinji!"

"See ya. Arika!"

* * *

As Shinji walked the rest of the way to his classroom, he thought. "For once in my life I have a friend. Arika Shimizu is my true friend."

And after all the misery in his life, Shinji felt happy. truly happy. However, his joy would not last, for tomorrow the test results would change everything for Arika and Shinji.

* * *

 **Next Chapter 2: More Than Human**


	3. Chapter 2: More than Human

**Well, the long wait is over. Time for the next chapter.**

 **Chapter 2: More Than Human**

* * *

In the commander's office at Nerv HQ, Gendo Ikari and his second-in-command, Kouzou Fuyutsuki, were viewing data on unit 00's current condition. They were interrupted by a woman's voice,

"I'm here with the status report, Commander."

Walking through the office door and up to the commander's desk was Ritsuko Akagi. Under her arm were several folders containing information on the test results of the P.E.C.T.

"Dr. Akagi. What is the status of the P.E.C.T.?" asked the commander.

"Well the results are in. A whole bunch of students have qualified to be future Eva pilots. However two stand out from the others. One is your own son with a score of 95%, which I'm sure you already know."

"And the other?"

"The other happens to be the new student that transferred from Tokyo 2. Arika Shimizu."

"And her score?"

"Her score couldn't be better. She has a 99.5%, which by all means is a 100% compatibility to the Lilith DNA."

With this statement, the commander under his steeped hands grinned.

"Excellent. File her as the primary test subject to become unit 01. Dispatch a group of section 2 agents to her home for her capture, once the school day ends. Then wipe all data and records related to her from the city."

"What about your son's score? He's also qualified for the Project: Evangelion Conversion Test, if I'm correct? " asked Fuyutsuki.

"Should the third child become a problem in the future and we're in need of another evangelion, then he'll become it."

"Ikari, are you also aware of the bond forming between your son and the test subject?"

"I was not. However, this will not to a problem because I'm sending him back to stay with his teacher while unit 01 is finalized. Enough about the third child! Back to the matter at hand. Dr. Akagi?"

"Yes sir?"

"In the meantime, you are to prepare the second test cage for the test subject and unit 01. Have the Lilith DNA injection and tranquilizer sedative ready. I want the B type equipment finished by the time the transformation stage is complete."

"What about the core?"

"We've taken care of that already. I'm warning you Dr. Akagi. Make no mistake with the tranquilizer sedative. Understood?"

"Yes sir."

"Then you are dismissed."

Ritsuko exited the office with haste. The commander grinned under his steeped hands and muttered,

"Good. With this, the child will be even further broken for the scenario by the disappearance of his new friend."

* * *

It was afternoon of Arika Shimizu's second day at Tokyo 3 High School, and she was feeling pretty good. During the day between classes, she talked to Shinji to try to encourage him out of his shell. She even joined him on the roof for lunch. Overall, she thought that Shinji was a good person, but he needed some social attention and to not bottle up all his emotions all the time. With her guidance and encouragement, he would be out of his shell in no time. Despite it being only her second day around Shinji, she was starting to feel a small attraction to the boy, an attraction that could only described as two lost souls coming together for the first time and finding each other to be their salvation.

After a final goodbye to Shinji, Arika headed home. As she walked, she thought about how yesterday she had not only saved someone's life but made a new friend in the process. She also felt good because she was positive that she passed the test with a really high score. However, this brought her mind back to the questions she had to answer.

"Now that I think of it, many of those questions were rather bizarre. I know simple athletic questions are understandable, but questions about my genetic makeup, a more detailed approach on appearance and thought process? Isn't some of that a bit… too much?!"

With a sigh, she shook her head and continued walking until she got home, not noticing the men in black suits hiding in the shadows.

Arika walked up the front steps and put her school bag down. Bending over and reaching into the bag, she searched for her door key. Finding it, she moved to unlock the door, only to find it slightly ajar. Now suspicious, she slowly opened the door the rest of the way. Looking into the house, her expression changed from one of caution to outright disbelief. Everything was gone. All of her and her grandmother's belongings had vanished. The walls were bare, and the floor clean where the furniture used to be. Nothing was left except for a coffee table in the living room. In the middle of the table was an envelope with her name inscribed on the front. She picked up the letter, quickly tore it open, and read the message inside aloud.

"Dear Shimizu Arika,

Congratulations on passing the Physical Evaluation Capability Test. Because of your exceptionally high score, you have been selected to be the primary candidate for Nerv's new top secret program. I'm sure you're wondering where everything in your house has gone, along with your grandmother. Well, she and it have been relocated to an onsite apartment. This is to make carrying out the operation will be easier.

You may wonder what the operation is about. To get straight to the point, because your score results were very high, you are now classified as the primary test subject for the Project: Evangelion Conversion Test. otherwise known as the P: E.C.T. By the time you finish reading this letter, Section 2 will be there to bring you into our custody. Farewell Shimizu Arika.

Forever may your world be changed.

Supreme Commander Gendo Ikari and P: E.C.T. Head Dr. Ritsuko Akagi."

As she read the last line, shaking with denial, she felt two people grab her from behind. She tried to escape them, but to no avail. In the scuffle, she dropped the letter and yelled in anger,

"No! You can't take me! Please! I don't want to be a part of this! I have a life worth living!"

The Section 2 agents forced her to the ground, their iron grip causing her great pain.

"Uoff! Mmhmhmm… No! Shinji needs me! Mmhmm … Stop! Mmhmhmm … STOP! … mmm … Help me! Somebody hel …"

An explosion rang in her head and everything faded to black for Arika.

"There. That'll take care of her," said the agent who had struck her with a blackjack.

"Orders are to take her to HQ for the procedure." said the head agent.

"Inform commander Ikari that the test subject is captured and is in route to Nerv."

* * *

A few hours later in the brig at Nerv headquarters, Arika began to stir. She slowly opened her eyes to find that she was in a dark cell. There was not much to look at in the small room. Four steel walls surrounded her, one with a reinforced door. On one side was a toilet with a sink and mirror next to it, and on the other, attached to the wall, was the rather uncomfortable bed she found herself on. She went to move a stray hair from her eyes only to find that her hands were cuffed behind her back. Pulling at the bonds, she found, was futile.

She heard multiple footsteps approaching her cell. The door was thrown violently open, and since she had no way to cover her eyes, the light from outside blinded her. Two Section 2 agents entered, grabbed her, and dragged her out into the light. When she could finally see again, there was a crowd around her: six agents in total, four guards, and a blond scientist in a lab coat. No words were exchanged among the group, but at a glare from the blond women, everyone moved. One of the guards jabbed their gun into her back, forcing her forward, and the whole group began marching through the halls of Nerv.

They marched until they reached a set of elevators. While waiting for an elevator to arrive, they stopped next to a room with caution tape spread across its large doorway. Peering through the doorway past the tape, Arika saw multiple consoles that were lit with only warning lights.. Beyond them was an observation window that had equipment thrown about behind it in a chamber with something that looked like blood covering some of the walls. Next to one of the doors was a chart of names, a brief description of the project they were conducting, and a stamp that read FAILED at the bottom of the page. Three things caught her attention in the description and made her remember what Shinji told her about his mother's death.

"He said that his mother died in a car accident and that they tried to revive her, but the project failed," she thought. The project title on the sheet read Yui Ikari Eva Core Revival and Retrieval Test, and judging by the stamp, the project didn't end well.

"He also said that his mother's name was Yui Ikari."

Putting two and two together, she realized with a shudder that that was the room where Shinji's mother had officially died.

* * *

The elevator then arrived, and the group filed on. As they descended, she could only think about the kinds of tests they were going to perform on her.

"What on earth are they doing here? What are they planning to do with someone like me? I mean, as far as I know, I'm not really special for the field of science, except for my mutated hair color. And that's not very interesting...'

Her thoughts were interrupted when the blond scientist said something about taking a route through the first test cage. This brought her attention to the now opening elevator doors. Passing through, she found herself in a giant chamber that was many stories tall. The catwalk they were walking on spanned the space. On the far side of the room, in restraints bolted to the wall, was a gigantic, humanoid shaped being, covered head to toe in thick yellow and white armor, with one eye. The scientist then spoke,

"This here is the first prototype of humanity's ultimate weapon of defense: Evangelion unit 00. Unit 00 is imperfect in a few ways, however. It deteriorates when put under major physical stress and has to be serviced and maintained frequently. To solve these problems, we created a new method of constructing an Evangelion. Using DNA mutations, we scale an already stable organism up to size."

"And what is this stable organism you speak of?"

"You'll find out soon enough."

The group continued to cross the catwalk. As they walked, aside from feeling the eyes from the guards behind her, Arika could also feel the stare of a greater presence. Glancing back past the guards and over the catwalk, she saw the prototype unit staring back at her with a warning look. She shivered and turned back as the group arrived at another set of elevators. One was labeled Test Cage 1 and another Test Cage 2. The blond scientist opened the Test Cage 2 elevator, and the group entered. When they reached the bottom, they stepped out into the large cage. As Arika looked around the great open space, she wondered, ''Why go through all the trouble of locking me in a cell, just to bring me here to an extremely large space where I could possibly escape?'

Her eyes then landed on a single metal chair bolted to the floor in the middle of the cage. Next to it were two tables, one with two different-sized syringes and a jar with biohazard labels on it. The other had a thick, rubbery looking wetsuit laid out on it with an opening in its back. She glanced down at herself, and saw she was wearing a similar, but thinner, version of the suit. She suddenly realized that she was practically naked, and her face reddened with embarrassment. The blond scientist moved to the table with the thick suit and then stood in front of Arika, with it in her hands. Realizing what was going to happen, With all her might, Arika tried to break free from the agents' grasp, but to no avail. The rest of the agents took hold of her or a part of the suit and forced her in. Her struggles only grew more futile as the parts of her in the suit were nearly impossible to move. The blond scientist stepped back once Arika was fully in the suit.

"There. With the malleable cybernetic contact and armored surface suit on, your movements are now mostly restricted for the next part of the procedure."

She then moved over to the other table, opened the biohazard jar, and filled the large needle completely with fluid. With a frightened voice, Arika asked, "What are you going to inject into me!?"

"I'm injecting a liquid sample of 100% DNA from the second angel, called Lilith to be specific. The DNA will change your biology to make you capable of fighting the rest of the angels in the future."

As the blond scientist came closer with the needle, Arika tried to resist and screamed in protest, but the doctor drained the entire syringe into her shoulder. Section 2 agents then moved to restrain her. Once Arika was strapped down in the chair, the fake blond grabbed the other needle. Infuriated form being stabbed once, Arika with the last of her strength tugged at the restraints, bumping into the doctor's arm with her head. Knocked off balance from the head-butt, the doctor dropped the syringe, which tumbled out of her hand and hit the floor with a crash.

"Shit! Damn you, you little brat! Everyone, evacuate the test cage immediately! The test subject hasn't been tranquilized!" she yelled.

As the group fled for the exit, Arika suddenly felt her strength triple. With a few tugs, she broke the straps as if they were thin as paper. Now free, she ran after the group, yelling, , "Come back here! I'm not letting you get away with this!"

"You're gonna payyyyyyoooow!" she cried, only getting a few feet\ before stumbling and falling to her hands and knees in pain. Struggling to get up but failing, she shouted, "WHAT HAVE YOU DONE TO ME YOU BITCH! Why!?"

Looking down, she noticed that the ground was starting to move further and further away from her face. She closed her eyes tightly as another intense wave of pain hit, lasting for a few minutes. Finally. when the pain had mostly stopped, she opened her eyes to find that she was now the size of a humanoid giant. An image of Unit 00 flashed through her mind, making her realize her fate. With this, she collapsed and fell into a deep sleep.

* * *

Back on the surface, walking to his new home after stopping at a convenience store to get food for dinner, Shinji reflected on the day spent with his new friend Arika. How they ate lunch together, how she would try to lighten his spirits, how they talked about each other's pasts. He just couldn't get her out of his head.

"She's being so nice to me. I wish there was something I could do to pay her back."

After he thought for a bit, an idea struck.

"Maybe I should make her a bento, since she doesn't seem to like the school's lunch. Yeah."

So the next morning, Shinji made a lunch to give to Arika. However, when he arrived at school, she wasn't there. He waited the whole day. and still she didn't show up for class. This left him concerned.

'Maybe she's sick? If she is, I hope she gets well.'

The next day, she still wasn't at school, and the next. With each day, Shinji became more and more worried. As he approached the mailbox to the apartment he was sharing. he thought, 'What if something happened to her? Where could she be?'

He noticed a letter sticking out of his mail slot. Taking the envelope, hoping it was from Arika, he opened it only for his heart to sink. In the letter, written in the center was 'Go back to live with your sensei. Signed Gendo Ikari.'

* * *

Meanwhile, more cybernetics were being implanted throughout Arika's newly massive body. An entry plug port was installed in her back just below her neck. To top it all off, restraints and many layers of armor were placed on her; transforming her into a titan with purple, black, and neon green highlights. Also, there was a helmet with a jagged tooth line and a single horn rising above the eyes, covering her head completely. All that was missing was the complex layered chest plate armor. Today, the core would be installed, and her transformation into an Eva would be complete. Technicians moved the core into a cavity cut in the middle of the chest. Within seconds the flesh around the red sphere bonded to it and healed around it. What they weren't expecting was that once the area had fully healed, the titanic being suddenly lurched to life.

It struggled to move, making its bonds begin to crack under pressure. One by one they broke, nothing keeping the beast at bay. It then roared an ear piercing, unholy, roar to the heavens. The berserker known as Unit 01 was born, full of pain and hatred.

* * *

 **Next: Chapter 3: Enlightenment I**


	4. Chapter 3: Enlightenment I

**A/N: I just started my first year of college and this took awhile to getting around to after settling in but here's the next chapter.**

* * *

 **Chapter 3: Enlightenment I**

* * *

 **A few minutes earlier…**

All she could feel was pain, a lot of pain… and she hated it. It was like someone had drilled a hole into her chest cavity with a molten iron pole. and then left her there as if they wanted her to die from severe internal burning and blood loss. Suddenly, she felt something protruding from her back, releasing an electric feeling throughout her body. Leaving her momentarily stunned, unprepared for the next sensation. Something then got shoved into the hole in her chest causing a wave of new and even more intense pain. She was brought back to reality by an announcement that projected through the cage she resided in.

" **Core insertion complete. Electrical levels remaining within the safety zone. Now moving to final phase. Begin chest plate installation."**

Arika's attention focused on the scientists and engineers working to move the chest plate armor into place. She could feel her arms and shoulders held in place by thick, metal bindings. Her legs and waist were similarly bound to a hard surface. With subtle movement, so as not to alert the people around her, she tilted her head down, getting a view of her lower body. She could see her reflection in an orange-red liquid that reached just below her chest. Looking on with horror, she could see that everywhere, except for her chest, which held a spherical red gem, was covered in purple, green and black armor, similar to that of unit 00. Covering her head completely was a helmet with a jagged mouth line and a single horn rising from the center of the forehead.

'No. This can't be happening!' her mind screamed in denial.

If anyone could have seen her facial expression, they would have noticed the shift from fear to pure rage. As the engineers prepared to install the chest plate armor, the restraints around the giant began to groan. Without warning, they started to break one by one. Everyone panicked and fled the chamber as Arika, now unit 01, broke free of her prison. Letting her pain be known, she roared out a cry of anguish. However, instead of a human shout, all the engineers and scientists heard an ear piercing low toned screatsh. A scientist in the control booth yelled, "Ejecting the power cable!" A _Thunk_ resounded through the change as the massive cable detached.

"One minute of internal battery remaining!"

Feeling the electrical sensation lessen, Arika realized that her ability to move was starting to wane. As she approached the control booth, with her tormentors inside, she reared back for a punch. She decided that she'd make them pay for turning her into a biomechanical abomination. She did not know, nor did anyone in the control room except the blond scientist and the commander, about the new evangelion's origin. Gendo Ikari smirked from his position.

'Finally. Unit 01 is born to serve its role in the senario. Let the child have its tantrum. for it won't affect the course of events. Soon the third child will be called here and then everything will fall into place. And so it begins. Soon I'll be with you again Yui.'

Unit 01 pounded the booth with punches, damaging the test cage wall and cracking the viewing widow's glass. With each punch, however, her strength faded. Her last strike bounced off the wall next to the window almost harmlessly. Her arm then fell to the side. Feeling her legs give out, she slumped over crashing to the cage floor and drifted into a deep sleep.

* * *

Or that's what seemed to happen on the outside.

Arika slowly opened her eyes and found herself lying on a flat surface. Looking up she saw a normal sky with clouds, only tinted red. Sitting up and turning her head about, she could see a horizon in the distance. She also noted that there didn't seem to be anything else sharing the space she currently was sitting in.

"Where am I and what is this place?" she spoke aloud, hearing her voice echo.

However, she didn't expect to get a response.

"Hello? Is someone there?"

Standing up and turning around, she saw a woman who looked to be in her late twenties wearing a lab coat over a simple dress. Her hair was dark brown, and reminded her of Shinji's. Yet something was off about her appearance as well. Dark red patches, like wounds, stained her clothing and covered the exposed skin of her body. Small ones pockmarked her face. Her form also appeared to be astral as it had some transparency to it. However, a calm aura radiated from her. despite her looking frail and on the verge of death. Arika suddenly realized that standing in front of her was Shinji's mother, looking as she had ten years ago when she died. With some hesitation, Arika asked, "You wouldn't happen to be Mrs. Ikari would you?"

"Indeed I am, and yet I am not at the same time. I'm merely a remnant of her soul and thoughts. Yui Ikari's dying wish if you will, manifested by the will of the all mother, in a clone of the second angel, Lilith's core… And who might you be young Lilum child, now the beast called Evangelion?"

"I'm Shimizu Arika, a close friend to Mrs. Ikari's son Shinji."

The remnant looked momentarily lost in memory at the mention of the woman's child, before exclaiming, "Oh that's great! My dear Shinji has gained a girlfriend in my absence. One that is true to the heart and saved him from great peril! She is deemed worthy in my eyes to be a companion of his choosing."

Arika started to blush after hearing the joyful statement but then frowned, remembering her predicament. She was now an armor-clad abomination, no one knew where she was, she didn't know where she was either, and Shinji was probably alone again needing help and worried sick about her disappearance.

"Unfortunately, he's alone again and probably wondering where I've gone. I promised that I'd be there for him if he needed help. What kind of friend am I if I can't support him in his time of need?!"

"Alas yes," the Yui remnant sighed. "He's alone again without your soul to guide him, child, but I don't think that will stop him from trying to be a better person in your absence."

It continued in a less emotional tone, "And to answer the question on your mind, we are in the plane of existence within an angel's-excuse me, an Evangelion's core. Here, thoughts are free to be heard by all individuals and souls appear as their heart's will. However, souls can only be here for three reasons. One, they can be forced here, Yui Ikari for example. Or two, they willed themselves here through their angelic power, like the all-mother did with me. Or three, the soul of the body, this core resides in willed themselves here, which I think happens to be your case. Further proof lies in the form of your presence here."

Looking down at herself, Arika saw that she now resembled a combination of the lithe young woman she was her new titanic form, wearing the black suit she was forced into with her new ruby red core in the center of her chest. If she could have seen her face, she would know that her light green hair was still just below shoulder length, but her once deep blue eyes now matched her hair. A feeling of urgency rose in her mind as she looked back to see the remnant's form begin to flicker.

"It seems I only have minutes now before I completely fade from all planes of existence." it addressed as a hopeful but sad look crossed its face.

"W-What do you mean your fading?! You can't go yet, I just met you here! I'll be alone again!" Arika cried.

In response, the remnant returned to Yui's personality and stated, "I'm sorry that I can't stay much longer but as we both know, I'm supposed to be dead. However, by the will of the second angel, my soul's disappearance has been delayed until now for a reason."

Though Arika was still stricken with sadness, she couldn't argue with that fact. Yui Ikari's time was up, and what was left of her soul needed to pass on and be at peace. Wiping the tears from her eyes, Arika looked again at the remnant bringing a sad smile to her face. Much to her surprise, as if the jumbled mess of mother, women, and scientist became one, it-no, she-donned a look of determination and sagely spoke to Arika one more time.

"What matters now Lilum child, is that you hear our final message. Do you care for Shinji? Because if you do then, as his mother, I want you to protect him. Protect him from the will of his own father. The man we once knew has fallen far from grace and will do anything, even bring about third impact. if he could see us again. However great dangers are yet to come. Fifteen children of the first angel Adam will come to this city in retaliation for humanity wronging the all-father. Each one is unique in its own way, but beware, while some may have strength. others may clash with the power of 'thunder'. Wipe them out before they reach the all-mother's domain or else all that what was and is will cease to be. Should you conquer Zeruel the angel of might and persuade Tabris that humanity should live on, then the all-mother will give you her blessing and reveal the untold truth of your existence. When the time is right, you must seek her out. Let her know you exist. With this I leave you to face the false prophecy of Seele's dead sea scrolls. Farewell Shimizu Arika. May you live through the end of days."

* * *

And with that, the remnant faded. leaving Arika once again alone, to ponder its parting words.

"Fifteen children of Adam… Zeruel angel of might… Tabris… the all-mother's blessing… Seele's dead sea scrolls… There's just too many things I must do! And what does she mean 'the untold truth of my existence?' What could I possibly not know about myself? Though when she said 'the end of days', that scares me. Could she be talking about third impact?"

The very thought of it sent a shiver up her spine. Supposedly, the second angel Lilith would have some answers for her once she made contact. However, for now there was not much to do besides thinking and sleeping. Deciding to test her possible new abilities, she forced her senses to the outside. Ever so slowly, the scenery inside the core vanished and the world around her faded into existence. In her limited range of view, she could see that she had been brought to a different location than the one where her transformation occurred.

On some of the walls were signs that read cage seven. In front of her was a wide catwalk spanning the width of the space with restraint arms running from it attached to the area between her neck and shoulders. Looking down, she saw she was almost neck deep in that red-orange liquid from earlier. As she attempted to move her arm, she felt not only resistance from the liquid, but weight against her shoulders, as well. Out of the corner of her eye on either side, she could see a long shape, somewhat like a pylon, of black mixed with green connected to each shoulder. These shoulder pylons were were bolted in the cage wall, restraining her arms. However, these restraints seemed less restrictive. They looked as if they just barely kept her in place. Her feet also felt locked to the floor below the liquid.

Glancing around the cage, Arika found that no personel seemed to be in with her. She listened for any noise to alert her of someone's presence, but the place was dead quiet. Only the faint sounds of machines running in the background could be heard. Despite this, she felt the subtle pressure that told her she was being watched from an unknown location. She pondered but decided that doing something rash like attempting escape would bring unwanted attention, so she opted to wait patiently for something to change or someone to walk through the door to the cage.

As time went on, boredom set in. Every now and then, she'd try to move a few of her muscles so she didn't get stiff. Once she tried to speak aloud, but all that came out was a intangible growl. Taking a nap didn't seem to work either. She'd close her eyes only to wake a few minutes later. As she contained to do nothing, apprehension, eagerness and eventually fear began manifesting in her mind. The gravity of her situation began to set in. No one was around to talk because it was probably night, no one would be able to understand her anyway, and now she was dying from isolation and boredom.

'Here I am, stuck as some giant human-like monster covered from head to toe in armor. Everything I feel about my body is off. I have no apparent hunger or thirst, and my energy feels limited, but my strength is infinite.'

If anyone could have listened, they would have heard her voice become more desperate and filled with anguish.

'Nearly nothing about me even feels remotely like my gender anymore! ... apart from my hair… Even that feels different! Like someone took scissors and cut it short! Stranger, I can feel the presence of the core in my chest! More importantly, it's probably been weeks. No, months since Shinji last saw me. He's probably worried sick and still doesn't know where I am, let alone what's happened to me! What am I going to do?!'

Her thoughts ended as she broke into sobs. Eventually, she cried herself in to another deep sleep.

* * *

Many months passed, but only two things of note happened. During the time, Nerv attempted the first pilot activation test of unit 01, which went off without a hitch, even though Arika was dormant inside the core. Also, Nerv staff was replaced so that no one knew of the evangelion's creation. FInally, Shinji had had enough, "Today," he told himself, "I stop waiting and wondering. Today, I find Arika."

He started by asking his sensei for her potential whereabouts, but he got no information relevance. Recalling Akira telling him that she used to live in Tokyo 2, Shinji went there and began to ask around. Through the day, he went from door to door, and street to street, even asking strangers passing by, giving a brief description each time. He went for days on end, covering a different section of the city each time. However, while he got some answers, most of the responses were worthless. Some people said she was homeschooled but only saw her every now and then. Others thought they had seen her lately, even the other day. These hints turned out to be red herrings leading him nowhere. A homeless man who Shinji had passed several times during the day gave him some unwanted advice, "Ya should'a just given up kid. See'n how much y'er try'n to find this lady friend of y'ers. I'd hate to break it to ya, but you'll find nut'n more here. Go on home kid."

But Shinji kept going, searching every nook and cranny he could find. He told himself he would not stop until he had a solid answer, but his obsession was starting to wear on him. After searching for nearly two weeks and covering most of the city, he decided he'd try one more time. He felt his luck was running dry and time was running out.

"Nothing. Not one person in this damn city knows where Arika is. Hell, with all the searching I've done for the past two weeks, I could've been just a few feet away from her residence."

He continued his journey back in silence, but with each step his frustration built until it reached a boiling point. Making matters worse, it dawned on him that one of the main reasons he couldn't find a trace of her was because he was looking in the wrong place. Kicking a pebble on the sidewalk as he stepped, he yelled out, "It's hopeless! The world is just too big to find just person who is important to me! Why did I even try when it all amounted to nothing?!"

A familiar voice played in the back of his head, calming him. Now now Shinji. Cheer up. Being pessimistic about it isn't going to get you anywhere…"

"Arika … " he sighed, calming down.

"Just who exactly are you?"

Looking up he found himself back at his "home" and in front of the mailbox. Looking at the box, he saw once again the indication that there was mail. Slowly he walked over, took his key out from his pocket, and unlocked the box. Inside was what looked to be a few manuals and a letter. Opening the envelope, he found an id pass with his picture and a piece of paper with the current date, 2015, with all but two lines of text blacked out. Shinji hadn't thought his heart could sink any lower, but it did. For the text simply read

"Come." "I have a use for you now."

* * *

At the same time, alone in the cage, deep inside of Nerv, sat the purple and green behemoth. If one were to listen closely, one could hear the faint sounds of crying as the feeling of foreboding set in. Something was coming. Deep in the waters of the pacific ocean, danger was hurtling towards Tokyo 3.

* * *

 **A/N: This concludes the intro and sets the stage for the canon. Where's Shinji going? Will Arika wake up? What could this danger possibly be? Who knows? Find out next in Chapter 4: Angel Attack.**


End file.
